That is a tough one. I've done this sort of thing before, but in 3D 
software, and I already had a displacement (black to white) map to use 
for extruding the 3D surface. I then used a procedural texture color 
gradient on the Y axis of the model to apply my chosen colors to the 
model's contours, which could be controlled by editing the spacing of 
colors within the gradient texture itself. The final step was to render 
the image from the top view in a parallel camera mode, producing a flat 
2D image with no perspective distortion. This could then be composited 
with the original topo map.

I don't see any easy way to automate part of this in GIMP, other than 
perhaps using a blur filter to help with the blending between contours 
(doubtful if that will even give great results). It's also hard to try 
without seeing an example map, because some topo maps are a pain this 
way - they often have things like numbers overlaid on the lines, which 
creates many little gaps that must be compensated for when selecting a 
specific area.

Hope you find a way.

Marc
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